Ministers have been accused of discriminating against dyslexic pupils by announcing plans to award 5% of marks in GCSE exams for spelling, punctuation and grammar as part of a drive to improve communication skills.

Dyslexia experts, educationists and teachers' unions say the new rules on marking, announced by the Department for Education last month, will penalise hundreds of thousands with a genuine spelling disability and make it more difficult for them to reach target grades.

At the same time dyslexia groups have reported mounting disquiet and confusion among parents and pupils, who are concerned at the lack of trained staff available in schools who can help them overcome their disadvantage and guide them on how to gain extra time, or other assistance, in exams.

In a white paper in 2010, the DfE expressed the government's determination to better equip young people for the jobs market by placing a greater emphasis on spelling, punctuation and grammar in GCSE marking. It stated: "When young people compete for jobs and enter the workplace, they will be expected to communicate precisely and effectively so we think that changes in the last decade to remove the separate assessment of spelling, punctuation and grammar from GCSE mark schemes were a mistake.

"We have asked Ofqual [the Office of Examinations and Qualifications Regulation] to advise on how mark schemes could take greater account of the importance of spelling, punctuation and grammar for examinations in all subjects."

Last month, Ofqual announced that for GCSE courses beginning in September, 5% of marks would be awarded for performance in spelling, punctuation and grammar in English literature, geography, history and religious studies.

A spokesman for Ofqual confirmed there would be no special exemptions from the marking regime for dyslexic pupils. However, as was the case previously, a pupil with a statement of special educational needs can gain up to 25% of extra time in exams. This can also be made available for a pupil with an evidence-backed recommendation from a suitably qualified teacher or psychologist. But the process of attaining extra time is difficult for many pupils and parents, particularly when expert help is not on hand in schools.

One headteacher of a large state comprehensive school said the change would mean that a pupil who had shown a good knowledge and understanding of, for example, history – but who had spelling problems due to dyslexia – could well end up with a worse grade than a good speller who had done less well on the history questions.

Dr Kate Saunders, chief executive of the British Dyslexia Association, said: "We are greatly concerned that these changes may penalise dyslexic individuals. We feel that it is discrimination. Dyslexic candidates are not seeking advantage but merely a level playing field in order to demonstrate their knowledge and skills. Our continuous efforts to improve conditions have now regressed."

In 2009 the then Labour government announced a £10m package to train 4,000 specialist dyslexia teachers over the following two years after a review of services for children with the learning difficulty, published by the education expert Sir Jim Rose. The BDA says that many of these specially trained teachers are now being made redundant. It has also had its government funding of £107,000 a year for a helpline withdrawn.

Christine Blower, general secretary of the National Union of Teachers, the largest teachers' union, said students for whom English was not their mother tongue would also suffer. "The proposed GCSE reforms to spelling, punctuation and grammar targets will make it difficult for students who have either English as a second language or are dyslexic."

In September last year the criteria for judging whether pupils could gain extra time for exams because of dyslexia were redefined because of suspicion that the system was being abused and that non-deserving cases were getting special treatment. Dyslexia groups say that this has left many parents and pupils confused about the rules.